Chlamydia trachomatis is an intracellular bacterium which infects around 129 million people annually. Despite similar infection rates between sexes, most research investigating the effects of chlamydial infection on fertility has focused on females. There is now emerging evidence of a potential link between Chlamydia and impaired male fertility. The only treatments for chlamydial infection are antibiotics, with azithromycin (AZI) being one of the commonly used drugs. However, recent studies have suggested that optimizing the treatment regime is necessary, as higher concentrations of AZI may be required to effectively clear the infection in certain cell types, particularly testicular macrophages. To address this challenge, we have prepared liposomes consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and D-α-tocopheryl polyethylene glycol 1000 succinate (TPGS) loaded with AZI for clearing Chlamydia. These liposomes exhibited stability over time and were readily taken up by both macrophages and epithelial cells. Moreover, they demonstrated significant enhancement of chlamydial clearance in both cell types. In a mouse model, the drug-loaded liposomes cleared Chlamydia within the penile urethra more efficiently than the same dose of unencapsulated drug. Furthermore, the liposome-drug treatment showed significant protective effects on sperm motility and morphology, suggesting potential benefits in reducing sperm damage caused by the infection.